It isn't handy to manage missions in different mission folder locations(i.e "C:\Program Files (x86)\Steam\steamapps\common\Arma 3\"). It's better to store all mission files in "Profile" root directory.
It's better to store all user oriented files in profile folder:
Profile:
--MPMissions - Global mp missions storage(this is for all users)
--MPMissionsCache - global online mission cather
--Users:
----User1:
------MPMissions - User1 own mp mission storage(this missions appears with globals in game list, merged with global folder)
----User2:
------MPMissions - User2 own mp mission storage(this missions appears with globals in game list, merged with global folder)